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Questions related from Silvia Caprari
Hi, I have a question about the 0.5 McFarland standard. In different websites I read that the for the 0.5 McFarland standard, the absorbance at a wavelength of 625 nm should be 0.08 to 0.13. I...
09 September 2018 4,881 1 View
Hi everyone, I would like to know how I can determine if a point significantly deviates from the linear regression when I plot the data in a scatter plot. I am using excel and I made a scatter...
07 July 2018 5,306 8 View
Hi all, i am new in image processing and using ImageJ. I want to measure the density in areas of pictures that were originally taken at a different magnification. I attached an example that I hope...
06 June 2018 7,297 4 View
Hi, I am new with Western Blot and I need a few clarifications about the use of blocking and incubation solution. I understood that blocking is done to saturate the membrane with proteins...
12 December 2017 4,432 4 View
Hi, I am preparing a sodium phosphate buffer solution at 0.1 M pH 7. For the preparation I am following this instruction that requires to mix 1 M Na2HPO4 and 1 M NaH2PO4 like this: 57.7 ml 1 M...
11 November 2017 6,569 3 View
Hi, I need some suggestions on which statistical tests are most appropriate for the analysis of my experiment. Basically I have plates with different antibiotic concentrations in the medium. The...
09 September 2017 8,214 15 View
Hi, I have a question about how to calculate the enzyme activity from absorbance. I have absorbance values for different concentrations of my samples at different times. As far as I understood, I...
09 September 2017 1,770 4 View
Hi all, I would like to ask you a question about the data analysis in an enzymatic activity assay. It is the first time I deal with this kind of stuff. I have a kit for the beta lactamase...
09 September 2017 1,233 5 View
Hi all, I have quite a stupid question about safety precautions when cutting out bands from an agarose gel under a UV transilluminator. I am aware that you need to wear lab coat, long sleeved...
06 June 2017 3,117 1 View
Hi all, I made different minipreps starting from the same sample of bacterial culture because my intention was to increase the concentration of plasmid in my final plasmid preparation. Now I have...
06 June 2017 3,052 4 View
Hi, I would like to have a clarification about the optimization of the condition reactions in a ligation.Why a larger amount of cut vector is used if plasmid is larger and a larger amount of...
06 June 2017 3,661 3 View
Hi, I am running PlasmidFinder on fasta files containing assembled contigs. The results seem to indicate the presence of two replicons in the same contig even if I am not completely sure of how...
05 May 2017 5,119 4 View
Hi all, I was wondering.Given the DNA sequence of a protein in bacteria, how can I determine where the signal peptide is in this sequence? I found servers that predict the position of the signal...
03 March 2017 4,811 3 View
Hi all, I was wondering why for most of the analyses with bacteria, e.g. the determination of a bacterial growth curve, they are first grown overnight in broth and then diluted in new broth to...
03 March 2017 410 4 View
Hi, can you explain me why the minimum inhibitory concentration is measured after overnight growth of the microorganism? Actually, I thought the MIC was measured during the log phase since the...
01 January 2017 9,988 16 View
Hi I have a few questions about the extraction of RNA and RT-qPCR. I am aware that the real time PCR is normally run on more replicates of the same sample. I was wondering how it is better to...
12 December 2016 2,147 4 View
Hi, I can't understand well the use of the normalization for analysing reverse transcriptase real-time pcr data and why you need to use housekeeping genes. Actually my issue is that I can't...
12 December 2016 5,273 6 View
Hi all, can you give me some examples of 7-base cutter restriction enzymes?I can't find a list specific for these. Also, I need to choose a 6-base cutter that works at same temperature and in the...
12 December 2016 2,252 0 View
Hi all, I extracted RNA from bacteria and I run an agarose gel on these samples. How do I recognize if I have RNA and not DNA? I have three bands (in attachment) and I am not sure about what they...
12 December 2016 3,301 13 View
Hi, do you know if it can happen that the plasmid sequence of a bacterium is "split" in different contigs coming from the ngs results?I have problems in trying to "foresee" the entire sequence of...
11 November 2016 2,021 5 View
Hi, can you tell me a few programs/tools for the assembly of plasmids starting from contigs coming from Illumina sequencing? I am working in Windows, so the program should run on this operative...
11 November 2016 8,801 0 View
Hi all, I have to prepare a stock solution of Sulfamethoxazole for Minimal inhibitory concentration experiments with bacteria. I can't understand very well how I have to dissolve the drug powder....
11 November 2016 2,060 4 View
Hi all, I am completely new in the field of Western Blot. I need antibodies directed against the bacterial gene "aac(6`)-Ib-cr" that codifies for a protein that is a fluroquinolone acetylating...
10 October 2016 9,818 5 View
Hi all, can you explain to me what the cloning primers are? are they also called"diagnostic"? for what purpose are they needed? Thanks
10 October 2016 882 0 View
Hi, I heard that the ng sequencing is more accurate than the Sanger sequencing in generating sequences. For example I heard that if I want to sequence a bacterial gene that I previously amplified...
10 October 2016 3,732 4 View
Hi all, I am trying to interpret the results coming from ngs on some bacterial isolates that are antibiotic resistant. This is completely new for me and I have different questions about it.I would...
10 October 2016 4,935 2 View
Hi all, I am trying to analyse sequencing results coming from ngs on bacterial strains. They were sequenced with the Illumina method. I got sequencing results in reads and contigs. This field is...
10 October 2016 1,701 4 View
Hi, I am studying some carbapenem resistant clinical isolates of Klebsiella. The resistance is probably due to plasmids that carry the resistance genes. These genes are usually found in insertion...
10 October 2016 3,955 10 View
Hi, I am used to preparing LB plates with antibiotic solution added to liquid medium and pour the mix into the plate.. I was wondering: is it the same if I spread the antibiotic solution on the LB...
10 October 2016 5,149 6 View
Hi all, I heard it is possible to clean the own DNA sample (after extraction) by performing a sort of "dialysis "with a floating filter disc in H2O...Can you explain me how it works and how this...
10 October 2016 4,760 1 View
Hi all, can you explain to me In which conditions it is better to choose a gradient gel instead of a normal one and why? Also, I read on the website of some companies providing gels for protein...
09 September 2016 6,931 0 View
Hi , can you tell me why Escherichia coli is always used as an experimental Organism? What features does it have to make it suitable for cloning and transformation, bacterial conjugation, protein...
09 September 2016 9,009 1 View
Hi all, I need to analyse results coming from next generation sequencing on bacterial 3 strains that are carbapenem-resistant. I am using the software "Artemis" to analyze the sequences. I...
09 September 2016 4,811 5 View
Hi,I am trying to visualize my DNA bands run on agarose gels (stained with gel red during the gel preparation). Although I am using UV fluorescence to visualize the gel, I think some setting in my...
09 September 2016 2,672 4 View
Hi all, I wanted to ask you where it is better to keep bacterial overnight cultures if you don't use them immediately. Let's say that I have overnight cultures and I want to streak them on plates...
09 September 2016 4,911 3 View
Hi, I have to cut some plasmids (natural plasmids)in order to determine the size on gel electrophoresis. I would like that the enzyme cuts the plasmid once, but I don't know the sequence of...
08 August 2016 3,782 3 View
Hi, I am trying to calculate the efficiency of transformation of my electrocompetent cells. To do that, I calculated the average of the colonies I obtained on tree plates streaked. I was wondering...
08 August 2016 906 2 View
Hi, do you know a protocol for the extraction of outer membrane proteins from Gram negative bacteria? I am working on Klebsiella pneumonia and I don't have a sonicator avalabale in my...
08 August 2016 9,802 8 View
Hi, I am analysing some data coming from genotyping I am performing on carbapenem- resistant isolates of K.pneumoniae. The resistance genes should be carried on plasmids and I looked for the...
08 August 2016 6,077 1 View
Hi, I am trying to get plasmid profiles from clinical isolates. I extracted them and visualized them in the gel electrophoresis. I tried to cut them with a 6bp enzyme XbaI to have more ideas on...
08 August 2016 1,164 2 View
Hi ..I run an agarose gel on a plasmidic extract and I have different bands. I don't know if they are different forms of the same plasmid or different plasmids. I want to determine if the bands...
08 August 2016 675 2 View
Hi, I run an agarose gel for 4 hours and I noticed that my bands after that time were more fainted. Gel Red has been added to the gel during the preparation and the DNA loading buffer was added to...
08 August 2016 825 3 View
Hi, I am struggling with my transformation experiments. I am studying bacterial strains that seem resistant to carbapenem antibiotics. What I did is the extraction of natural plasmids (because the...
07 July 2016 5,021 7 View
Hi all, I run a PCR to look for an integron in different bacterial isolates to test the presence of this integron in the bacterial genome. This integron is often associated with resistance...
07 July 2016 8,099 3 View
Hi, I am doing transformation experiments with plasmidic extract and I am using DH5a cells for the transformation..I obtained few colonies on a plate with 1 ug/ml of meropenem antibiotic. Anyway,...
07 July 2016 528 3 View
Hi all, I want to do electroporation experiments with plasmidic extract (natural plasmids) from Klesbiella pneumoniae strains that seem resistant to carbapenem antibiotics to prove that the...
07 July 2016 8,021 1 View
Hi all, I am doing transformation experiments with plasmids extracted from the bacterium Klebsiella pneumoniae to confirm that the resistance genes are carried on the plasmids. I was wondering,...
07 July 2016 3,916 1 View
Hi, do you know what the endemic and epidemic plasmids are and the difference between them? Thanks
07 July 2016 5,794 0 View
Hi, I have to do conjugation experiments to see if the resistance is transferred by plasmids. I don't have a strain in lab to be used as acceptor for my conjugation experiments, so I have to buy...
07 July 2016 7,631 4 View
Hi all, can anyone explain me why for some procedures it is better to use bacteria in log-phase and for other ones bacteria in stationary phase? For example for DNA and plasmid purification you...
07 July 2016 8,288 5 View
Hi all, I attached a picture of an agarose gel because I can't obtain straight bands, especially when I run my ladder (first and last well). They form a sort of wave. I run DNA samples on 1%...
07 July 2016 6,240 11 View
Hi, I have a doubt about the cloning of antibiotic resistance genes. how do I choose the antibiotics to add to the medium when I need to select the recombinant clones? I know that one antibiotic...
07 July 2016 5,256 5 View
Hi all, can you give me some opinions/ suggestions on why my agarose gel comes out like this on the bottom after the run? It always happens to me with the larger gels, never with the small ones....
07 July 2016 1,811 7 View
Hi all, in your opinion is it a problem that I have an EDTA solution at 9.5 instead of 8 for plasmidic extraction? I added more NaOH to dissolve the powder because at Ph 8 there still were not...
06 June 2016 1,374 2 View
Hi all, I am extracting plasmids from my bacteria. They are natural plasmids and I don't know the size, nor the sequence. I am trying to make plasmid profiles. I run the gel on the extracts in...
06 June 2016 9,929 7 View
Hi all, if a protocol says "resuspend in 400 ul of 50 mM Tris.HCl containing 100m M sodium acetate" , is it ok what I did as reported here following? for a final volume of 10 ml: I mixed 500 ul of...
06 June 2016 7,769 0 View
Hi all, I am trying to extract natural plasmids from my bacterial strains. I don't know the size of plasmids, nor if different plasmids are present in the same strain. I run a gel with the...
06 June 2016 9,349 7 View
Hi all, I have to separate bacterial plasmids (after extraction) on agarose gel. Which electrophoresis conditions would you suggest me to use (in terms of hours, voltage)? Thanks
06 June 2016 5,874 5 View
Hi all, I am extracting natural plasmids from my bacteria. I don't know the size, nor the sequence. I am trying to determine plasmid profiles of the bacterial isolates I have. I have bands on...
06 June 2016 7,956 5 View
Hi all, is this following calculation correct ? I need 0.5 ug of DNA for a restriction digestion and I have an initial concentration of DNA of 696 ng/ul. The total volume of the restriction...
06 June 2016 3,198 3 View
Hi, do you have experience in RAPD? It is completely new for me and I have to use it to type my bacteria strains. I am aware that I have to use random primers. My questions are1) How can I design...
05 May 2016 1,470 4 View
Hi all,Do you know why carbapenems (and other antibiotics) are considered last-resort drug?I am aware that they are used when all the other drugs fail to treat infections but I don't understand...
05 May 2016 4,027 8 View
Hi all, can anyone suggest me a method-protocol to understand if a bacterial gene is on the genomic or plasmidic DNA?I have done PCR on purified DNA sample (that contains both genomic and plasmdic...
05 May 2016 6,576 5 View
Hi all, I anticipate that I am completely new and for the first time I have to do cloning of genes whose sequence is unknown (The final objective is indeed to sequence the gene). Since I am not...
05 May 2016 8,278 1 View
Hi all, Are you familiar with Bioedit in the visualization of the sequences? I am trying to read sequences coming from Sanger sequencing method and I was said that the "genuine" sequence is...
05 May 2016 2,510 3 View
